Transcriptome: A Tool for Biotechnological Applications of Quorum Sensing Using Single Cell and Viruses

  • Bhagwan Rekadwad


Cutting edge sequencing (NGS) technology is a sound methodologically for exploration of information of to carry out advanced research in the various field of biology such as microbiology, biotechnology, agricultural microbiology, microbial ecology and community analyses for determination of cellular activities and gene expression under adverse environmental conditions. For the transcriptome analyses and its quantification, RNA-Seq has provided unlimited access to modern bio-analysis. This chapter presents an awful description of quorum sensing, quorum quenching, transcriptome analyses, NGS and correlation as well as an association of microorganism with other organisms such as human, plants, animal, microorganisms (eukaryotes and prokaryotes) and viruses are explained as well. Thus, transcriptome analysis widens the possibilities to get more in-depth/to get more top to bottom information about the modern RNA world in genetically similar cells or in single cell and viruses.


Quorum sensing Quorum quenching Plant-microbe interactions Next generation sequencing Microbiome Single cell genomics 


Dtr machinery

DNA transfer and replication machinery


N-(3-hydroxy-octanoyl)-homoserine lactone (3OH,C8-HSL)


Type-4 secretion system


  1. Basavaraju M, Sisnity VS, Palaparthy R, Addanki PK (2016) Quorum quenching: signal jamming in dental plaque biofilms. J Dent Sci 11:349–352. Scholar
  2. Cabezón E, Ripoll-Rozada J, Peña A, de la Cruz F, Arechaga I (2015) Towards an integrated model of bacterial conjugation. FEMS Microbiol Rev 39:81–95. Scholar
  3. Chaparro JM, Badri DV, nVivanco JM (2014) Rhizosphere microbiome assemblage is affected by plant development. ISME J 8:790–803. Scholar
  4. Charbonneau ARL, Forman OP, Cain AK, Newland G, Robinson C, Boursnell M, Parkhill J, Leigh MDJ, Waller AS (2017) Defining the ABC of gene essentiality in streptococci. BMC Genomics 18:426. Scholar
  5. Deng Q, Ramsköld D, Reinius B, Sandberg R (2014) Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells. Science 343:193–196. Scholar
  6. Dey SS, Kester L, Spanjaard B, Bienko M, van Oudenaarden A (2015) Integrated genome and transcriptome sequencing of the same cell. Nat Biotechnol 33:295–292. Scholar
  7. Erez Z, Steinberger-Levy I, Shamir M, Doron S, Stokar-Avihail A, Peleg Y, Melamed S, Leavitt A, Savidor A, Albeck S, Amitai G, Sorek R (2017) Communication between viruses guides lysis–lysogeny decisions. Nature 541:488–493. Scholar
  8. Feltner JB, Wolter DJ, Pope CE, Groleau M, Smalley NE, Greenberg EP, Mayer-Hamblett N, Burns J, Déziel E, Hoffman LR, Dandekar AA (2016) LasR variant cystic fibrosis isolates reveal an adaptable quorum sensing hierarchy in Pseudomonas aeruginosa. MBio 7:e01513-16. Scholar
  9. Ghosh D, Roy K, Williamson KE, Srinivasiah S, Wommack KE, Radosevich M (2009) Acyl-homoserine lactones can induce virus production in lysogenic bacteria: an alternative paradigm for prophage induction. Appl Environ Microbiol 75:7142–7152. Scholar
  10. Gonzalez JE, Keshwan ND (2006) Messing with bacterial quorum sensing. Microbiol Mol Biol Rev 70:859–875. Scholar
  11. González-Torres P, Pryszcz LP, Santos F, Martínez-García M, Gabaldón T, Antón J (2015) Interactions between closely related bacterial strains are revealed by deep transcriptome sequencing. Appl Environ Microbiol 81:8445–8456. Scholar
  12. Grün D, Kester L, van Oudenaarden A (2014) Validation of noise models for single-cell transcriptomics. Nat Methods 11:637–640. Scholar
  13. Guan S, Rosenecker J (2017) Nanotechnologies in delivery of mRNA therapeutics using nonviral vector-based delivery systems. Gene Ther.
  14. Hao X, Xie P, Johnstone L, Miller SJ, Rensing C, Wei G (2012) Genome sequence and mutational analysis of plant-growth-promoting bacterium Agrobacterium tumefaciens CCNWGS0286 isolated from a Zinc-Lead mine tailing. Appl Environ Microbiol 78:5384–5394. Scholar
  15. Hargreaves KR, Kropinski AM, Clokie MRJ (2014) What does the talking? Quorum sensing signalling genes discovered in a bacteriophage genome. PLoS One 9:e85131. Scholar
  16. Hartmann A, Rothballer M, Hense BA, Schröder P (2014) Bacterial quorum sensing compounds are important modulators of microbe-plant interactions. Front Plant Sci 5:131. Scholar
  17. Høyland-Kroghsbo NM, Mærkedahl RB, Svenningsen SL (2013) A quorum-sensing-induced bacteriophage defense mechanism. MBio 4:e00362-12. Scholar
  18. Junker JP, van Oudenaarden A (2014) Every cell is special: genome-wide studies add a new dimension to single-cell biology. Cell 157:8–11. Scholar
  19. Kalia VC (2014) Microbes, antimicrobials and resistance: the battle goes on. Indian J Microbiol 54:1–2. Scholar
  20. Kalia VC (2015) Microbes: the most friendly beings? In: Kalia VC (ed) Quorum sensing vs quorum quenching: a battle with no end in sight. Springer, New Delhi, pp 1–5. Scholar
  21. Kalia VC, Kumar P (2015) Genome wide search for biomarkers to diagnose Yersinia infections. Indian J Microbiol 55:366. Scholar
  22. Kalia VC, Kumar P, Pandian SK, Sharma P (2014) Biofouling control by quorum quenching. Hb_25. In: Kim SK (ed) Springer handbook of marine biotechnology, vol 15. Springer, Berlin, pp 431–440Google Scholar
  23. Kalia VC, Prakash J, Koul S, Ray S (2017) Simple and rapid method for detecting biofilm forming bacteria. Indian J Microbiol 57:109–111. Scholar
  24. Kaur G, Rajesh S, Princy SA (2015) Plausible drug targets in the Streptococcus mutans quorum sensing pathways to combat dental biofilms and associated risks. Indian J Microbiol 55:349. Scholar
  25. Kim HS, Lee S, Byun Y, Park HD (2015) 6-Gingerol reduces Pseudomonas aeruginosa biofilm formation and virulence via quorum sensing inhibition. Sci Rep 5:8656. Scholar
  26. Kim MK, Zhao A, Wang A, Brown ZZ, Muir TW, Stone HA, Bassler BL (2017) Surface-attached molecules control Staphylococcus aureus quorum sensing and biofilm development. Sci Rep 2:17080. Scholar
  27. Kothari R, Singh RP, Kothari V (2016) Application of next generation sequencing technologies in revealing plant-microbe interactions. Next Gener Seq Applic 3:1. Scholar
  28. Koul S, Kalia VC (2017) Multiplicity of quorum quenching enzymes: a potential mechanism to limit quorum sensing bacterial population. Indian J Microbiol 57:100–108. Scholar
  29. Koul S, Prakash J, Mishra A, Kalia VC (2016) Potential emergence of multi-quorum sensing inhibitor resistant (MQSIR) bacteria. Indian J Microbiol 56:1–18. Scholar
  30. Krause S, Bremges A, Münch PC, McHardy AC, Gescher J (2017) Characterisation of a stable laboratory co-culture of acidophilic nanoorganisms. Sci Rep 7:3289. Scholar
  31. Kumar R, Verma H, Haider S, Bajaj A, Sood U, Ponnusamy K, Nagar S, Shakarad MN, Negi RK, Singh Y, Khurana JP, Gilbert JA, Lal R (2017) Comparative genomic analysis reveals habitat-specific genes and regulatory hubs within the genus Novosphingobium. mSystems 2:e00020-17. Scholar
  32. Long SW, Olsen RJ, Eagar TN, Beres SB, Zhao P, Davis JJ, Brettin T, Xia F, Musser (2017) Population genomic analysis of 1,777 extended-spectrum beta-lactamase-producing Klebsiella pneumoniae isolates, Houston, Texas: unexpected abundance of clonal group 307. MBio 8:e00489-17. Scholar
  33. Majumdar S, Pal S (2017) Bacterial intelligence: imitation games, time-sharing, and long-range quantum coherence. J Cell Commun Signal.
  34. Mellbye BL, Giguere AT, Bottomley PJ, Sayavedra-Soto LA (2016) Quorum quenching of Nitrobacter winogradskyi suggests that quorum sensing regulates fluxes of nitrogen oxide(s) during nitrification. MBio 7:e01753-16. Scholar
  35. Mendes LW, Kuramae EE, Navarrete AA, Van Veen JA, Tsai SM (2014) Taxonomical and functional microbial community selection in soybean rhizosphere. ISME J 8:1577–1587. Scholar
  36. Mhedbi-Hajri N, Yahiaoui N, Mondy S, Hue N, Pélissier F, Faure D, Dessaux Y (2016) Transcriptome analysis revealed that a quorum sensing system regulates the transfer of the pAt megaplasmid in Agrobacterium tumefaciens. BMC Genomics 17:661. Scholar
  37. Mondy S, Lalouche O, Dessaux Y, Faure D (2013) Genome sequence of the quorum-sensing-signal-producing nonpathogen Agrobacterium tumefaciens strain P4. Genome Announc 1:e00798–e00713. Scholar
  38. Pérez J, Buchanan A, Mellbye B, Ferrell R, Chang JH, Chaplen F, Bottomley PJ, Arp DJ, Sayavedra-Soto LA (2015) Interactions of Nitrosomonas europaea and Nitrobacter winogradskyi grown in co-culture. Arch Microbiol 197:79–89. Scholar
  39. Picelli S, Björklund AK, Faridani OR, Sagasser S, Winberg G, Sandberg R (2013) Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nat Methods 10:1096–1098. Scholar
  40. Prateeksha SBR, Shoeb M, Sharma S, Naqvi AH, Gupta VK, Singh BN (2017) scaffold of selenium nanovectors and honey phytochemicals for inhibition of Pseudomonas aeruginosa quorum sensing and biofilm formation. Front Cell Infect Microbiol 7:93. Scholar
  41. Ray S, Kalia VC (2017) Biomedical applications of polyhydroxyalkanaotes. Indian J Microbiol 57:39–47. Scholar
  42. Rekadwad BN, Khobragade CN (2017a) Bacterial quorum sensing (QS) in rhizosphere (paddy soil): understanding soil signaling and N- recycling for increased crop production. In: Kalia VC (ed) Microbial applications vol.2 – biomedicine, agriculture and industry. Springer Nature, New Delhi, pp 119–131. Scholar
  43. Rekadwad BN, Khobragade CN (2017b) Microbial biofilm: role in crop productivity. In: Kalia VC (ed) Microbial applications vol.2 – biomedicine, agriculture and industry. Springer International Publishing, Cham., AG, Springer Nature, pp 107–118. Scholar
  44. Sayavedra-Soto L, Ferrell R, Dobie M, Mellbye B, Chaplen F, Buchanan A, Chang J, Bottomley P, Arp D (2015) Nitrobacter winogradskyi transcriptomic response to low and high ammonium concentrations. FEMS Microbiol Lett 362:1–7. Scholar
  45. Schikora A, Schenk ST, Hartmann A (2016) Beneficial effects of bacteria-plant communication based on quorum sensing molecules of the N-acyl homoserine lactone group. Plant Mol Biol 90:605–612. Scholar
  46. Seymour JR, Amin SA, Raina JB, Stocker R (2017) Zooming in on the phycosphere: the ecological interface for phytoplankton–bacteria relationships. Nat Microbiol 2:17065. Scholar
  47. Shapiro E, Biezuner T, Linnarsson S (2013) Single-cell sequencing-based technologies will revolutionize whole-organism science. Nat Rev Genet 14:618–630. Scholar
  48. Shen Q, Gao J, Liu J, Liu S, Liu Z, Wang Y, Guo B, Zhuang X, Zhuang G (2016) A new acyl-homoserine lactone molecule generated by Nitrobacter winogradskyi. Sci Rep 6:22903. Scholar
  49. Shirota M, Kinoshita K (2016) Discrepancies between human DNA, mRNA and protein reference sequences and their relation to single nucleotide variants in the human population. Database (Oxford) 2016:baw124. Scholar
  50. Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N, Wang X, Bodeau J, Tuch BB, Siddiqui A, Lao K, Surani MA (2009) mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods 6:377–382. Scholar
  51. Wei G, Yu J, Wang J, Gu P, Birch DS, Chen Y (2016) Hairpin DNA-functionalized gold nanorods for mRNA detection in homogenous solution. J Biomed Opt 21:097001. Scholar
  52. Welsh MA, Blackwell HE (2016) Chemical probes of quorum sensing: from compound development to biological discovery. FEMS Microbiol Rev 40:774–794. Scholar
  53. Wu AR, Neff NF, Kalisky T, Dalerba P, Treutlein B, Rothenberg ME, Mburu FM, Mantalas GL, Sim S, Clarke MF, Quake SR (2014) Quantitative assessment of single-cell RNA-sequencing methods. Nat Methods 11:41–46. Scholar
  54. Zhu H, He CC, Chu QH (2011) Inhibition of quorum sensing in Chromobacterium violaceum by pigments extracted from Auricularia auricular. Lett Appl Microbiol 52:269–274. Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  • Bhagwan Rekadwad
    • 1
  1. 1.National Centre for Microbial Resource, National Centre for Cell SciencePuneIndia

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